Looking at the files, it looks like Indoctrination relies on the Ethics Attraction mechanics that shifts your own pops ethics.
Normally, primitives don't have Ethics attraction, but when you set to Indoctrinate, you activate the mechanic in regards to your ethics and actually just give their civilization a massive ethics pull to those ethics (factor of 20 if you are fanatic. For relevance, the normal factor for your pops as a fanatic yourself is 3) plus increasing the speed in which their pops drift by a factor of 3. Once one of their shifts to that ethic, within 12 months you get an event that triggers their shift change as a civ.
Also looks like Indoctrination can't shift their ethics to fanatic, only to regular ethics. So if you are F. Materialist and they shift to Materialist, you can stop because that's as far as they will go. EDIT: Looks like I read the event wrong; With 1 pop, it will drift to normal, when 2 or more pops are that ethic, it will drift to Fanatic, even if you yourself are not fanatic
Also looks like (and I'll be reporting this in the bug forums shortly) You cannot reliably drift primitive pops to Egalitarian unless you are Xenophile, because the Factor modifiers check for Xenophile, not Egalitarian (it can still happen, it just will be veeery slow compared to your other ethics)